Hi there,
I am reading the following paper to learn 3D-RISM
(1)Nguyen, C.; Yamazaki, T.; Kovalenko, A.; Case, D. A.; Gilson, M. K.;
Kurtzman, T.; Luchko, T. A Molecular Reconstruction Approach to Site-Based
3D-RISM and Comparison to GIST Hydration Thermodynamic Maps in an Enzyme
Active Site. Plos One 2019, 14 (7), e0219473.
https://doi.org/10.1371/journal.pone.0219473.
For the paper, the following command is used to calculated the density and
energy distributions.
$AMBERHOME/bin/rism3d.snglpnt \
- --prmtop fxa-strip.parm7 \
- --traj fxa-strip.nc --xvv cTIP3P_pse3.xvv \
- --entropicDecomp --molReconstruct \
- --guv g \
- --exchem exchem --entropy entropy --solvene solvene --potUV potUV \
- --exchemUC exchemUC \
- --solvcut 999999. --buffer 24. --tolerance 1e-2,1e-6 \
- --closure kh,pse2,pse3 --uccoeff
0.0327564,-3.26166,-0.000507492,0.0100166 \
- --mdiis_restart 100.0 --mdiis_nvec 10\
- --centering 3 \
- --verbose 2 > rism.out
There are 4 files which are molecular reconstructed
entropy.mol.1.dx
potUV.mol.1.dx
solvene.mol.1.dx
exchem.mol.1.dx
Which output file is related to "Water-water energy density distributions",
"Solute-water energy density distributions", and "Total water energy
density distributions"?
Best
Zhenting
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Received on Sun Oct 17 2021 - 04:00:03 PDT
